Refactor so that GenotypeAnnotation and InfoFieldAnnotation share common superclass VariantAnnotatorAnnotation

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java

@@ -15,7 +15,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import java.util.*;
 
 
-public class AlleleBalanceBySample implements GenotypeAnnotation, ExperimentalAnnotation {
+public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
 
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g) {
         Double ratio = annotateSNP(stratifiedContext, vc, g);

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java

@@ -22,7 +22,7 @@ import java.util.List;
 import java.util.Map;
 
 
-public class DepthPerAlleleBySample implements GenotypeAnnotation, StandardAnnotation {
+public class DepthPerAlleleBySample extends GenotypeAnnotation implements StandardAnnotation {
 
     private static String REF_ALLELE = "REF";
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java

@@ -49,7 +49,7 @@ import java.util.Map;
  * Time: 6:46:25 PM
  * To change this template use File | Settings | File Templates.
  */
-public class MappingQualityZeroBySample implements GenotypeAnnotation {
+public class MappingQualityZeroBySample extends GenotypeAnnotation {
     public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref,
                                         AlignmentContext context, VariantContext vc, Genotype g) {
         if ( g == null || !g.isCalled() )

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadDepthAndAllelicFractionBySample.java

@@ -52,7 +52,7 @@ import java.util.Map;
  * Time: 3:59:27 PM
  * To change this template use File | Settings | File Templates.
  */
-public class ReadDepthAndAllelicFractionBySample implements GenotypeAnnotation {
+public class ReadDepthAndAllelicFractionBySample extends GenotypeAnnotation {
 
         private static String REF_ALLELE = "REF";
 

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java

@@ -10,15 +10,12 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import java.util.List;
 import java.util.Map;
 
-public interface GenotypeAnnotation {
+public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation {
 
     // return annotations for the given contexts/genotype split by sample
-    public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g);
+    public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g);
-
-    // return the FORMAT keys
-    public List<String> getKeyNames();
 
     // return the descriptions used for the VCF FORMAT meta field
-    public List<VCFFormatHeaderLine> getDescriptions();
+    public abstract List<VCFFormatHeaderLine> getDescriptions();
 
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -10,16 +11,10 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import java.util.List;
 import java.util.Map;
 
-@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator INFO-field annotations", summary = "VariantAnnotator annotations, written to INFO Field")
+public abstract class InfoFieldAnnotation extends VariantAnnotatorAnnotation {
-public abstract class InfoFieldAnnotation {
-
     // return annotations for the given contexts split by sample
     public abstract Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc);
 
-    // return the INFO keys
-    public abstract List<String> getKeyNames();
-
     // return the descriptions used for the VCF INFO meta field
     public abstract List<VCFInfoHeaderLine> getDescriptions();
-
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java

@@ -0,0 +1,41 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
+
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.util.List;
+import java.util.Map;
+
+@DocumentedGATKFeature(enable = true, groupName = "VariantAnnotator annotations", summary = "VariantAnnotator annotations")
+public abstract class VariantAnnotatorAnnotation {
+    // return the INFO keys
+    public abstract List<String> getKeyNames();
+}